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A population genomics approach to the study of speciation in flowering columbines

A POPULATION GENOMICS APPROACH TO THE STUDY OF SPECIATION IN
FLOWERING COLUMBINES
by
Elizabeth Cooper
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(MOLECULAR BIOLOGY)
May 2011
Copyright 2011 Elizabeth Cooper

Aquilegia formosa and Aquilegia pubescens are two closely-related species belonging to the columbine genus. Despite their morphological and ecological differences, previous studies have revealed a large degree of intercompatibility as well as little sequence divergence between these two taxa, and the genetic mechanisms underpinning reproductive isolation remain unknown. In order to assess the feasibility of a full genome scan for speciation genes, inter- and intraspecific patterns of variation were compared for 9 nuclear loci; it was concluded that the two species were practically indistinguishable at the level of DNA sequence polymorphism, indicating either very recent speciation or continued gene flow. As a comparison, the variation at two loci was analyzed across 30 other Aquilegia species, revealing slightly more differentiation among taxa and evidence for isolation by geographic distance (which was not the case on a more local geographic scale).; The extremely low levels of genetic variation found between A. formosa and A. pubescens at neutral loci was deemed ideal for a genome-wide scan for allele frequency differences, so this was done using Solexa deep sequencing of pooled samples from each species. Polymorphisms were identified and annotated based on alignment with the A. coerulea reference genome, and SNPs with extreme values of allele frequency differentiation (>93.5%) were selected as candidate speciation genes. Two of these extreme SNPs caused amino acid changes in MYB and UGT proteins, both of which are known components of the anthocyanin (pigmentation) pathway.

A POPULATION GENOMICS APPROACH TO THE STUDY OF SPECIATION IN
FLOWERING COLUMBINES
by
Elizabeth Cooper
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(MOLECULAR BIOLOGY)
May 2011
Copyright 2011 Elizabeth Cooper